Alternatively, you can disable throttle checking using the -Si cputhrchk 0 configure switch. If you don't, and throttling is on, configure will fail.

OK, continuing with the build, in your build/ directory:

.././configure --prefix=/opt/ATLAS -A AMD64

Before you continue, domake xprint_enums ; ./xprint_enums
and study the output -- you might find a better ARCH fit than e.g. AMD64. If so, run the configure command above again. There is a lot of other options which you can configure as well. Obviously, nothing prevents you from experimenting and re-compiling if something goes wrong. You can also run without any -A switch at all.

Continuing:makemake installcp lib/lib* /opt/ATLAS/lib
Your libs should be in /opt/ATLAS/lib -- when you compiled something to include the new libs, use
"-L/opt/ATLAS/lib"